Starting phenix.real_space_refine on Fri Aug 22 18:36:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xdn_38282/08_2025/8xdn_38282.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xdn_38282/08_2025/8xdn_38282.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xdn_38282/08_2025/8xdn_38282.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xdn_38282/08_2025/8xdn_38282.map" model { file = "/net/cci-nas-00/data/ceres_data/8xdn_38282/08_2025/8xdn_38282.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xdn_38282/08_2025/8xdn_38282.cif" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 34 5.16 5 C 4454 2.51 5 N 1177 2.21 5 O 1228 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6894 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2193 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 13, 'TRANS': 273} Chain: "B" Number of atoms: 2193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2193 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 13, 'TRANS': 273} Chain: "C" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 332 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "D" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 332 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "E" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 193 Classifications: {'peptide': 24} Link IDs: {'TRANS': 23} Chain: "F" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 193 Classifications: {'peptide': 24} Link IDs: {'TRANS': 23} Chain: "G" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 409 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 4, 'TRANS': 46} Chain: "H" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 409 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 4, 'TRANS': 46} Chain: "I" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 287 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "J" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 287 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'FUD': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.76, per 1000 atoms: 0.26 Number of scatterers: 6894 At special positions: 0 Unit cell: (82.9026, 92.9514, 137.334, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 34 16.00 P 1 15.00 O 1228 8.00 N 1177 7.00 C 4454 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.54 Conformation dependent library (CDL) restraints added in 365.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1584 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 2 sheets defined 31.5% alpha, 35.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 83 through 86 removed outlier: 3.616A pdb=" N CYS A 86 " --> pdb=" O PHE A 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 83 through 86' Processing helix chain 'A' and resid 87 through 92 Processing helix chain 'B' and resid 87 through 92 removed outlier: 3.671A pdb=" N GLU B 92 " --> pdb=" O ARG B 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 96 Processing helix chain 'C' and resid 96 through 109 Processing helix chain 'D' and resid 73 through 109 removed outlier: 3.574A pdb=" N MET D 77 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LEU D 97 " --> pdb=" O MET D 93 " (cutoff:3.500A) Proline residue: D 98 - end of helix Processing helix chain 'E' and resid 42 through 60 Processing helix chain 'F' and resid 42 through 61 Processing helix chain 'G' and resid 6 through 39 removed outlier: 5.724A pdb=" N ILE G 28 " --> pdb=" O ARG G 24 " (cutoff:3.500A) Proline residue: G 29 - end of helix Processing helix chain 'G' and resid 49 through 53 Processing helix chain 'H' and resid 6 through 39 removed outlier: 5.259A pdb=" N ILE H 28 " --> pdb=" O ARG H 24 " (cutoff:3.500A) Proline residue: H 29 - end of helix Processing helix chain 'H' and resid 48 through 53 removed outlier: 3.617A pdb=" N LEU H 53 " --> pdb=" O VAL H 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 17 through 49 Proline residue: I 42 - end of helix Processing helix chain 'J' and resid 17 through 49 Proline residue: J 42 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 351 through 355 removed outlier: 3.625A pdb=" N LYS A 351 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N LYS A 102 " --> pdb=" O LEU A 358 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ILE A 360 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N THR A 104 " --> pdb=" O ILE A 360 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LEU A 172 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLN A 181 " --> pdb=" O PHE A 185 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N PHE A 185 " --> pdb=" O GLN A 181 " (cutoff:3.500A) removed outlier: 13.699A pdb=" N VAL A 186 " --> pdb=" O ASP A 209 " (cutoff:3.500A) removed outlier: 11.079A pdb=" N ASP A 209 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N TRP A 188 " --> pdb=" O ASN A 207 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N SER A 214 " --> pdb=" O PRO A 208 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLY A 215 " --> pdb=" O ARG A 239 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG A 239 " --> pdb=" O GLY A 215 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASP A 319 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N LEU A 339 " --> pdb=" O LYS A 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 101 through 108 removed outlier: 6.338A pdb=" N GLN B 181 " --> pdb=" O PHE B 185 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N PHE B 185 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 13.801A pdb=" N VAL B 186 " --> pdb=" O ASP B 209 " (cutoff:3.500A) removed outlier: 10.784A pdb=" N ASP B 209 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N TRP B 188 " --> pdb=" O ASN B 207 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N SER B 214 " --> pdb=" O PRO B 208 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU B 229 " --> pdb=" O ILE B 225 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA B 230 " --> pdb=" O LYS B 253 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS B 351 " --> pdb=" O ASN B 346 " (cutoff:3.500A) 452 hydrogen bonds defined for protein. 1299 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.84 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1226 1.32 - 1.45: 1789 1.45 - 1.57: 3967 1.57 - 1.69: 2 1.69 - 1.82: 58 Bond restraints: 7042 Sorted by residual: bond pdb=" CG1 ILE J 28 " pdb=" CD1 ILE J 28 " ideal model delta sigma weight residual 1.513 1.434 0.079 3.90e-02 6.57e+02 4.12e+00 bond pdb=" N LYS D 105 " pdb=" CA LYS D 105 " ideal model delta sigma weight residual 1.459 1.481 -0.022 1.19e-02 7.06e+03 3.47e+00 bond pdb=" CB ARG H 11 " pdb=" CG ARG H 11 " ideal model delta sigma weight residual 1.520 1.568 -0.048 3.00e-02 1.11e+03 2.59e+00 bond pdb=" CB ARG D 82 " pdb=" CG ARG D 82 " ideal model delta sigma weight residual 1.520 1.568 -0.048 3.00e-02 1.11e+03 2.54e+00 bond pdb=" CB VAL A 324 " pdb=" CG1 VAL A 324 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.46e+00 ... (remaining 7037 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 9282 2.26 - 4.53: 178 4.53 - 6.79: 30 6.79 - 9.05: 16 9.05 - 11.31: 3 Bond angle restraints: 9509 Sorted by residual: angle pdb=" N LYS D 105 " pdb=" CA LYS D 105 " pdb=" C LYS D 105 " ideal model delta sigma weight residual 111.07 104.91 6.16 1.07e+00 8.73e-01 3.32e+01 angle pdb=" CA MET C 77 " pdb=" CB MET C 77 " pdb=" CG MET C 77 " ideal model delta sigma weight residual 114.10 122.42 -8.32 2.00e+00 2.50e-01 1.73e+01 angle pdb=" CA GLU C 104 " pdb=" CB GLU C 104 " pdb=" CG GLU C 104 " ideal model delta sigma weight residual 114.10 122.22 -8.12 2.00e+00 2.50e-01 1.65e+01 angle pdb=" CB ARG H 11 " pdb=" CG ARG H 11 " pdb=" CD ARG H 11 " ideal model delta sigma weight residual 111.30 120.30 -9.00 2.30e+00 1.89e-01 1.53e+01 angle pdb=" CA GLN C 75 " pdb=" CB GLN C 75 " pdb=" CG GLN C 75 " ideal model delta sigma weight residual 114.10 121.74 -7.64 2.00e+00 2.50e-01 1.46e+01 ... (remaining 9504 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 3477 17.95 - 35.89: 486 35.89 - 53.84: 177 53.84 - 71.78: 33 71.78 - 89.73: 14 Dihedral angle restraints: 4187 sinusoidal: 1717 harmonic: 2470 Sorted by residual: dihedral pdb=" CA ASP A 153 " pdb=" CB ASP A 153 " pdb=" CG ASP A 153 " pdb=" OD1 ASP A 153 " ideal model delta sinusoidal sigma weight residual -30.00 -89.20 59.20 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CB GLU C 109 " pdb=" CG GLU C 109 " pdb=" CD GLU C 109 " pdb=" OE1 GLU C 109 " ideal model delta sinusoidal sigma weight residual 0.00 89.73 -89.73 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CA ASP A 280 " pdb=" CB ASP A 280 " pdb=" CG ASP A 280 " pdb=" OD1 ASP A 280 " ideal model delta sinusoidal sigma weight residual -30.00 -85.94 55.94 1 2.00e+01 2.50e-03 1.06e+01 ... (remaining 4184 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 646 0.037 - 0.073: 283 0.073 - 0.110: 99 0.110 - 0.147: 28 0.147 - 0.184: 6 Chirality restraints: 1062 Sorted by residual: chirality pdb=" CB THR D 103 " pdb=" CA THR D 103 " pdb=" OG1 THR D 103 " pdb=" CG2 THR D 103 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.42e-01 chirality pdb=" CA GLU C 104 " pdb=" N GLU C 104 " pdb=" C GLU C 104 " pdb=" CB GLU C 104 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.15e-01 chirality pdb=" CA LYS D 105 " pdb=" N LYS D 105 " pdb=" C LYS D 105 " pdb=" CB LYS D 105 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.22e-01 ... (remaining 1059 not shown) Planarity restraints: 1199 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU D 109 " 0.013 2.00e-02 2.50e+03 2.62e-02 6.88e+00 pdb=" C GLU D 109 " -0.045 2.00e-02 2.50e+03 pdb=" O GLU D 109 " 0.017 2.00e-02 2.50e+03 pdb=" N GLN D 110 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 226 " -0.033 5.00e-02 4.00e+02 4.92e-02 3.87e+00 pdb=" N PRO B 227 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 227 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 227 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 331 " 0.010 2.00e-02 2.50e+03 1.95e-02 3.80e+00 pdb=" C LYS B 331 " -0.034 2.00e-02 2.50e+03 pdb=" O LYS B 331 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU B 332 " 0.011 2.00e-02 2.50e+03 ... (remaining 1196 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 535 2.74 - 3.28: 6559 3.28 - 3.82: 11204 3.82 - 4.36: 12881 4.36 - 4.90: 23298 Nonbonded interactions: 54477 Sorted by model distance: nonbonded pdb=" OE1 GLN H 10 " pdb=" NE2 GLN H 14 " model vdw 2.195 3.120 nonbonded pdb=" O ASN F 44 " pdb=" ND2 ASN F 48 " model vdw 2.199 3.120 nonbonded pdb=" O VAL C 99 " pdb=" OG1 THR C 103 " model vdw 2.201 3.040 nonbonded pdb=" O LEU I 37 " pdb=" OG1 THR I 41 " model vdw 2.205 3.040 nonbonded pdb=" O GLN B 182 " pdb=" NH2 ARG G 24 " model vdw 2.207 3.120 ... (remaining 54472 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 75 through 361) selection = chain 'B' } ncs_group { reference = (chain 'C' and resid 72 through 111) selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.000 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 7042 Z= 0.200 Angle : 0.849 11.313 9509 Z= 0.443 Chirality : 0.048 0.184 1062 Planarity : 0.005 0.049 1199 Dihedral : 19.554 89.728 2603 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.31 % Allowed : 45.11 % Favored : 52.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.30), residues: 852 helix: 1.73 (0.33), residues: 254 sheet: -0.85 (0.27), residues: 396 loop : -0.65 (0.45), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG I 21 TYR 0.029 0.002 TYR B 221 PHE 0.018 0.002 PHE A 356 TRP 0.010 0.001 TRP C 86 HIS 0.010 0.002 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00460 ( 7042) covalent geometry : angle 0.84900 ( 9509) hydrogen bonds : bond 0.09832 ( 452) hydrogen bonds : angle 6.80757 ( 1299) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 209 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.7676 (ttm) cc_final: 0.7252 (ttm) REVERT: A 265 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7420 (mm) REVERT: A 296 ASP cc_start: 0.7659 (p0) cc_final: 0.7255 (p0) REVERT: B 249 SER cc_start: 0.6639 (m) cc_final: 0.6291 (p) REVERT: C 76 LYS cc_start: 0.7248 (mmtm) cc_final: 0.6949 (mmtt) REVERT: C 100 VAL cc_start: 0.8021 (p) cc_final: 0.7703 (m) REVERT: D 77 MET cc_start: 0.5241 (tpt) cc_final: 0.4211 (mtm) REVERT: D 82 ARG cc_start: 0.4288 (tmt-80) cc_final: 0.1508 (mtp85) REVERT: E 43 ARG cc_start: 0.6781 (ttt180) cc_final: 0.5995 (ptt-90) REVERT: E 52 PHE cc_start: 0.4945 (t80) cc_final: 0.4295 (t80) REVERT: G 44 MET cc_start: 0.4935 (ppp) cc_final: 0.4496 (pmm) REVERT: H 44 MET cc_start: 0.1728 (ppp) cc_final: 0.1280 (ppp) REVERT: J 39 ARG cc_start: 0.4715 (mmm160) cc_final: 0.4388 (mtp180) outliers start: 17 outliers final: 3 residues processed: 217 average time/residue: 0.4768 time to fit residues: 109.3377 Evaluate side-chains 178 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 174 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 257 ASN Chi-restraints excluded: chain A residue 265 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.2980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.3980 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN F 48 ASN ** G 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.202362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.159024 restraints weight = 7759.169| |-----------------------------------------------------------------------------| r_work (start): 0.4260 rms_B_bonded: 2.98 r_work: 0.4106 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.4106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7042 Z= 0.160 Angle : 0.723 9.284 9509 Z= 0.372 Chirality : 0.045 0.154 1062 Planarity : 0.005 0.050 1199 Dihedral : 8.572 52.362 995 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 8.56 % Allowed : 36.96 % Favored : 54.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.30), residues: 852 helix: 1.90 (0.32), residues: 265 sheet: -0.82 (0.27), residues: 396 loop : -0.81 (0.46), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 239 TYR 0.017 0.002 TYR H 33 PHE 0.013 0.001 PHE I 31 TRP 0.010 0.001 TRP B 259 HIS 0.005 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 7042) covalent geometry : angle 0.72293 ( 9509) hydrogen bonds : bond 0.03907 ( 452) hydrogen bonds : angle 5.94276 ( 1299) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 185 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.5464 (pp20) cc_final: 0.4733 (tm-30) REVERT: A 124 ILE cc_start: 0.7493 (OUTLIER) cc_final: 0.7286 (tp) REVERT: A 234 GLU cc_start: 0.7471 (pt0) cc_final: 0.7213 (pt0) REVERT: A 296 ASP cc_start: 0.7959 (p0) cc_final: 0.7542 (p0) REVERT: B 234 GLU cc_start: 0.5595 (OUTLIER) cc_final: 0.5300 (pt0) REVERT: B 249 SER cc_start: 0.6799 (m) cc_final: 0.6272 (p) REVERT: B 289 GLU cc_start: 0.7468 (tp30) cc_final: 0.7211 (tp30) REVERT: C 76 LYS cc_start: 0.7420 (mmtm) cc_final: 0.6546 (mmtt) REVERT: D 77 MET cc_start: 0.5255 (tpt) cc_final: 0.4462 (mtm) REVERT: D 82 ARG cc_start: 0.4238 (tmt-80) cc_final: 0.1537 (mtp85) REVERT: D 108 MET cc_start: 0.6448 (ppp) cc_final: 0.6194 (ppp) REVERT: E 43 ARG cc_start: 0.6802 (ttt180) cc_final: 0.5972 (ptt-90) REVERT: E 52 PHE cc_start: 0.5111 (t80) cc_final: 0.4850 (t80) REVERT: F 45 LEU cc_start: 0.7278 (OUTLIER) cc_final: 0.7064 (mm) REVERT: F 57 TRP cc_start: 0.5331 (OUTLIER) cc_final: 0.4872 (t-100) REVERT: G 44 MET cc_start: 0.4999 (ppp) cc_final: 0.4723 (pmm) REVERT: I 21 ARG cc_start: 0.8499 (tpt170) cc_final: 0.8153 (tpp80) REVERT: J 19 LYS cc_start: 0.8557 (tptt) cc_final: 0.8092 (tptm) outliers start: 63 outliers final: 29 residues processed: 222 average time/residue: 0.4333 time to fit residues: 102.0300 Evaluate side-chains 202 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 169 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 90 CYS Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 57 TRP Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 14 GLN Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain J residue 34 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 19 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 9 optimal weight: 0.2980 chunk 7 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 6 optimal weight: 8.9990 chunk 81 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 51 optimal weight: 0.0060 chunk 33 optimal weight: 2.9990 chunk 1 optimal weight: 0.3980 overall best weight: 1.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN E 48 ASN E 61 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.199558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.155229 restraints weight = 7719.761| |-----------------------------------------------------------------------------| r_work (start): 0.4219 rms_B_bonded: 2.68 r_work: 0.4074 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 7042 Z= 0.181 Angle : 0.750 16.378 9509 Z= 0.378 Chirality : 0.045 0.146 1062 Planarity : 0.005 0.050 1199 Dihedral : 8.318 54.605 991 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 8.83 % Allowed : 35.73 % Favored : 55.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.30), residues: 852 helix: 1.80 (0.32), residues: 265 sheet: -0.94 (0.26), residues: 396 loop : -0.80 (0.47), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 38 TYR 0.016 0.002 TYR B 221 PHE 0.020 0.002 PHE G 21 TRP 0.010 0.001 TRP A 259 HIS 0.008 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 7042) covalent geometry : angle 0.75030 ( 9509) hydrogen bonds : bond 0.03810 ( 452) hydrogen bonds : angle 5.76198 ( 1299) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 185 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.5556 (pp20) cc_final: 0.4822 (tm-30) REVERT: A 124 ILE cc_start: 0.7634 (OUTLIER) cc_final: 0.7367 (tp) REVERT: A 234 GLU cc_start: 0.7467 (pt0) cc_final: 0.7221 (pt0) REVERT: A 296 ASP cc_start: 0.7835 (OUTLIER) cc_final: 0.7595 (p0) REVERT: B 234 GLU cc_start: 0.5628 (OUTLIER) cc_final: 0.5012 (pt0) REVERT: B 249 SER cc_start: 0.6903 (m) cc_final: 0.6181 (p) REVERT: B 250 LEU cc_start: 0.7003 (mp) cc_final: 0.6429 (tp) REVERT: B 254 TYR cc_start: 0.7121 (OUTLIER) cc_final: 0.6109 (m-80) REVERT: B 296 ASP cc_start: 0.6912 (m-30) cc_final: 0.6626 (p0) REVERT: C 76 LYS cc_start: 0.7193 (mmtm) cc_final: 0.6921 (mmpt) REVERT: D 77 MET cc_start: 0.5231 (tpt) cc_final: 0.4434 (mtm) REVERT: D 82 ARG cc_start: 0.4204 (tmt-80) cc_final: 0.1334 (mtp85) REVERT: D 108 MET cc_start: 0.6524 (ppp) cc_final: 0.6294 (ppp) REVERT: E 43 ARG cc_start: 0.7025 (OUTLIER) cc_final: 0.6006 (ptt-90) REVERT: H 24 ARG cc_start: 0.6443 (ttt90) cc_final: 0.6235 (ttt90) outliers start: 65 outliers final: 32 residues processed: 226 average time/residue: 0.4458 time to fit residues: 106.7703 Evaluate side-chains 213 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 176 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 257 ASN Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 90 CYS Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 254 TYR Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 43 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 40 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 53 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 20 optimal weight: 0.0970 chunk 82 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 ASN F 48 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.201431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.157615 restraints weight = 7780.120| |-----------------------------------------------------------------------------| r_work (start): 0.4249 rms_B_bonded: 2.86 r_work: 0.4092 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 7042 Z= 0.147 Angle : 0.719 11.237 9509 Z= 0.363 Chirality : 0.044 0.145 1062 Planarity : 0.005 0.052 1199 Dihedral : 7.971 58.183 991 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 7.07 % Allowed : 37.91 % Favored : 55.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.30), residues: 852 helix: 2.04 (0.32), residues: 263 sheet: -0.89 (0.26), residues: 402 loop : -0.44 (0.49), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 11 TYR 0.011 0.001 TYR B 221 PHE 0.019 0.001 PHE G 27 TRP 0.008 0.001 TRP A 259 HIS 0.009 0.001 HIS B 112 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 7042) covalent geometry : angle 0.71899 ( 9509) hydrogen bonds : bond 0.03460 ( 452) hydrogen bonds : angle 5.48637 ( 1299) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 185 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.5584 (pp20) cc_final: 0.4835 (tm-30) REVERT: B 249 SER cc_start: 0.6901 (m) cc_final: 0.6544 (p) REVERT: B 250 LEU cc_start: 0.6940 (mp) cc_final: 0.6425 (tp) REVERT: B 254 TYR cc_start: 0.7111 (OUTLIER) cc_final: 0.6138 (m-80) REVERT: B 296 ASP cc_start: 0.6867 (m-30) cc_final: 0.6546 (p0) REVERT: C 72 PHE cc_start: 0.7246 (OUTLIER) cc_final: 0.6782 (t80) REVERT: C 76 LYS cc_start: 0.7472 (mmtm) cc_final: 0.7040 (mmpt) REVERT: D 76 LYS cc_start: 0.6047 (mmtm) cc_final: 0.5340 (tptt) REVERT: D 77 MET cc_start: 0.5375 (tpt) cc_final: 0.4578 (mtm) REVERT: D 82 ARG cc_start: 0.4332 (tmt-80) cc_final: 0.1572 (mtp85) REVERT: E 43 ARG cc_start: 0.7116 (OUTLIER) cc_final: 0.5944 (ptt-90) outliers start: 52 outliers final: 29 residues processed: 214 average time/residue: 0.4643 time to fit residues: 105.1746 Evaluate side-chains 209 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 177 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 257 ASN Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 90 CYS Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 254 TYR Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain E residue 43 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain I residue 40 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 60 optimal weight: 0.4980 chunk 76 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 chunk 52 optimal weight: 0.0870 chunk 21 optimal weight: 0.0970 chunk 15 optimal weight: 0.2980 chunk 11 optimal weight: 3.9990 overall best weight: 0.7958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 ASN F 48 ASN ** H 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.200912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.159637 restraints weight = 7834.474| |-----------------------------------------------------------------------------| r_work (start): 0.4268 rms_B_bonded: 2.75 r_work: 0.4064 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.4064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7042 Z= 0.152 Angle : 0.740 11.183 9509 Z= 0.370 Chirality : 0.045 0.170 1062 Planarity : 0.005 0.062 1199 Dihedral : 7.840 58.922 991 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 7.61 % Allowed : 37.77 % Favored : 54.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.30), residues: 852 helix: 1.90 (0.32), residues: 263 sheet: -0.83 (0.26), residues: 400 loop : -0.45 (0.50), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 11 TYR 0.015 0.002 TYR H 33 PHE 0.015 0.001 PHE A 356 TRP 0.008 0.001 TRP A 259 HIS 0.012 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 7042) covalent geometry : angle 0.73988 ( 9509) hydrogen bonds : bond 0.03397 ( 452) hydrogen bonds : angle 5.46629 ( 1299) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 183 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.5663 (pp20) cc_final: 0.4917 (tm-30) REVERT: A 265 LEU cc_start: 0.8229 (mm) cc_final: 0.7887 (mm) REVERT: B 249 SER cc_start: 0.6951 (m) cc_final: 0.6613 (p) REVERT: B 250 LEU cc_start: 0.6999 (mp) cc_final: 0.6526 (tp) REVERT: B 254 TYR cc_start: 0.7165 (OUTLIER) cc_final: 0.6153 (m-80) REVERT: B 296 ASP cc_start: 0.6921 (m-30) cc_final: 0.6553 (p0) REVERT: C 75 GLN cc_start: 0.7501 (pt0) cc_final: 0.7165 (pm20) REVERT: C 76 LYS cc_start: 0.7521 (mmtm) cc_final: 0.6998 (mmpt) REVERT: D 76 LYS cc_start: 0.6142 (mmtm) cc_final: 0.5428 (tptt) REVERT: D 77 MET cc_start: 0.5468 (tpt) cc_final: 0.4708 (mtm) REVERT: D 82 ARG cc_start: 0.4535 (tmt-80) cc_final: 0.1699 (mtp85) REVERT: E 43 ARG cc_start: 0.7184 (OUTLIER) cc_final: 0.5947 (ptt180) REVERT: E 57 TRP cc_start: 0.6744 (t60) cc_final: 0.6379 (t60) REVERT: H 10 GLN cc_start: 0.8158 (pp30) cc_final: 0.7551 (pp30) REVERT: H 14 GLN cc_start: 0.7694 (OUTLIER) cc_final: 0.7353 (pm20) outliers start: 56 outliers final: 33 residues processed: 215 average time/residue: 0.4765 time to fit residues: 108.6433 Evaluate side-chains 212 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 176 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 257 ASN Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 90 CYS Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 254 TYR Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain E residue 43 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain H residue 14 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 76 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 68 optimal weight: 0.0570 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 HIS A 321 ASN ** H 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.200810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.159437 restraints weight = 7826.897| |-----------------------------------------------------------------------------| r_work (start): 0.4267 rms_B_bonded: 2.73 r_work: 0.4066 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.4066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7042 Z= 0.150 Angle : 0.740 13.580 9509 Z= 0.371 Chirality : 0.045 0.168 1062 Planarity : 0.005 0.053 1199 Dihedral : 7.728 58.688 991 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 6.79 % Allowed : 39.40 % Favored : 53.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.30), residues: 852 helix: 1.79 (0.33), residues: 263 sheet: -0.74 (0.26), residues: 400 loop : -0.44 (0.49), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 11 TYR 0.015 0.002 TYR J 34 PHE 0.026 0.001 PHE G 27 TRP 0.008 0.001 TRP A 259 HIS 0.009 0.001 HIS B 112 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 7042) covalent geometry : angle 0.74005 ( 9509) hydrogen bonds : bond 0.03429 ( 452) hydrogen bonds : angle 5.42583 ( 1299) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 184 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.5595 (pp20) cc_final: 0.4842 (tm-30) REVERT: A 124 ILE cc_start: 0.7638 (OUTLIER) cc_final: 0.7391 (tp) REVERT: A 265 LEU cc_start: 0.8249 (mm) cc_final: 0.7894 (mm) REVERT: B 249 SER cc_start: 0.6978 (m) cc_final: 0.6679 (p) REVERT: B 250 LEU cc_start: 0.7076 (mp) cc_final: 0.6560 (tp) REVERT: B 254 TYR cc_start: 0.7217 (OUTLIER) cc_final: 0.6187 (m-80) REVERT: C 75 GLN cc_start: 0.7571 (pt0) cc_final: 0.7199 (pm20) REVERT: C 76 LYS cc_start: 0.7573 (mmtm) cc_final: 0.6986 (mmpt) REVERT: D 76 LYS cc_start: 0.6105 (mmtm) cc_final: 0.5424 (tptt) REVERT: D 77 MET cc_start: 0.5448 (tpt) cc_final: 0.4695 (mtm) REVERT: D 82 ARG cc_start: 0.4504 (tmt-80) cc_final: 0.1689 (mtp85) REVERT: E 43 ARG cc_start: 0.7160 (OUTLIER) cc_final: 0.5978 (ptt180) REVERT: E 57 TRP cc_start: 0.6757 (t60) cc_final: 0.6390 (t60) REVERT: G 44 MET cc_start: 0.3827 (pp-130) cc_final: 0.3373 (pmm) REVERT: H 10 GLN cc_start: 0.8147 (pp30) cc_final: 0.7539 (pp30) REVERT: H 14 GLN cc_start: 0.7605 (OUTLIER) cc_final: 0.7281 (pm20) outliers start: 50 outliers final: 30 residues processed: 214 average time/residue: 0.4897 time to fit residues: 111.1050 Evaluate side-chains 207 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 173 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 257 ASN Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 90 CYS Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 254 TYR Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain E residue 43 ARG Chi-restraints excluded: chain H residue 14 GLN Chi-restraints excluded: chain H residue 52 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 6 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 7 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 HIS A 321 ASN E 48 ASN ** H 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.197420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.154006 restraints weight = 7806.151| |-----------------------------------------------------------------------------| r_work (start): 0.4202 rms_B_bonded: 2.84 r_work: 0.4048 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 7042 Z= 0.201 Angle : 0.801 17.629 9509 Z= 0.399 Chirality : 0.047 0.205 1062 Planarity : 0.005 0.052 1199 Dihedral : 7.981 57.646 991 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 8.02 % Allowed : 38.59 % Favored : 53.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.30), residues: 852 helix: 1.62 (0.33), residues: 263 sheet: -0.71 (0.26), residues: 396 loop : -0.57 (0.48), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 11 TYR 0.013 0.002 TYR B 237 PHE 0.018 0.002 PHE A 356 TRP 0.011 0.001 TRP A 259 HIS 0.007 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00472 ( 7042) covalent geometry : angle 0.80083 ( 9509) hydrogen bonds : bond 0.03744 ( 452) hydrogen bonds : angle 5.64358 ( 1299) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 176 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.5551 (pp20) cc_final: 0.4968 (tm-30) REVERT: A 124 ILE cc_start: 0.7695 (OUTLIER) cc_final: 0.7406 (tp) REVERT: A 217 LEU cc_start: 0.6839 (OUTLIER) cc_final: 0.6411 (mm) REVERT: A 265 LEU cc_start: 0.8374 (mm) cc_final: 0.8056 (mm) REVERT: B 112 HIS cc_start: 0.6225 (p-80) cc_final: 0.5943 (p-80) REVERT: B 167 GLN cc_start: 0.6611 (OUTLIER) cc_final: 0.6411 (tp-100) REVERT: B 249 SER cc_start: 0.7153 (m) cc_final: 0.6795 (p) REVERT: B 250 LEU cc_start: 0.6999 (mp) cc_final: 0.6511 (tp) REVERT: B 254 TYR cc_start: 0.7252 (OUTLIER) cc_final: 0.6163 (m-80) REVERT: C 76 LYS cc_start: 0.7564 (mmtm) cc_final: 0.7102 (mmpt) REVERT: D 77 MET cc_start: 0.5382 (tpt) cc_final: 0.4689 (mtm) REVERT: D 82 ARG cc_start: 0.4399 (tmt-80) cc_final: 0.1154 (mmt180) REVERT: E 43 ARG cc_start: 0.7155 (OUTLIER) cc_final: 0.5992 (ptt-90) REVERT: E 57 TRP cc_start: 0.6773 (t60) cc_final: 0.6322 (t60) REVERT: G 44 MET cc_start: 0.3857 (pp-130) cc_final: 0.2783 (pmm) REVERT: H 10 GLN cc_start: 0.8177 (pp30) cc_final: 0.7905 (pp30) outliers start: 59 outliers final: 36 residues processed: 215 average time/residue: 0.4855 time to fit residues: 110.7734 Evaluate side-chains 213 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 172 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 90 CYS Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 254 TYR Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 267 GLN Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain E residue 43 ARG Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 52 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 46 optimal weight: 3.9990 chunk 75 optimal weight: 0.0870 chunk 37 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 ASN C 75 GLN ** H 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.197655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.153958 restraints weight = 7860.849| |-----------------------------------------------------------------------------| r_work (start): 0.4210 rms_B_bonded: 2.75 r_work: 0.4040 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.4040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 7042 Z= 0.220 Angle : 0.841 18.502 9509 Z= 0.424 Chirality : 0.048 0.213 1062 Planarity : 0.005 0.052 1199 Dihedral : 8.131 57.755 991 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 8.56 % Allowed : 38.72 % Favored : 52.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.30), residues: 852 helix: 1.21 (0.32), residues: 266 sheet: -0.71 (0.26), residues: 396 loop : -0.51 (0.49), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 239 TYR 0.012 0.002 TYR A 194 PHE 0.028 0.002 PHE G 27 TRP 0.013 0.002 TRP A 322 HIS 0.008 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00514 ( 7042) covalent geometry : angle 0.84081 ( 9509) hydrogen bonds : bond 0.03932 ( 452) hydrogen bonds : angle 5.82031 ( 1299) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 169 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.7752 (ttm) cc_final: 0.7365 (ttm) REVERT: A 217 LEU cc_start: 0.6911 (OUTLIER) cc_final: 0.6700 (mm) REVERT: A 265 LEU cc_start: 0.8354 (mm) cc_final: 0.8013 (mm) REVERT: A 329 GLU cc_start: 0.6817 (OUTLIER) cc_final: 0.5176 (mm-30) REVERT: B 167 GLN cc_start: 0.6743 (OUTLIER) cc_final: 0.6519 (tp-100) REVERT: B 250 LEU cc_start: 0.7042 (mp) cc_final: 0.6513 (tp) REVERT: C 76 LYS cc_start: 0.7648 (mmtm) cc_final: 0.7176 (mmpt) REVERT: D 77 MET cc_start: 0.5498 (tpt) cc_final: 0.4826 (mtm) REVERT: D 82 ARG cc_start: 0.4464 (tmt-80) cc_final: 0.3645 (mmm160) REVERT: E 43 ARG cc_start: 0.6996 (OUTLIER) cc_final: 0.5730 (ptt180) REVERT: E 57 TRP cc_start: 0.6786 (t60) cc_final: 0.6586 (t60) REVERT: E 60 ARG cc_start: 0.6027 (mtt90) cc_final: 0.5557 (mtt90) REVERT: G 44 MET cc_start: 0.3639 (pp-130) cc_final: 0.2887 (pmm) REVERT: H 10 GLN cc_start: 0.8222 (pp30) cc_final: 0.7823 (pp30) REVERT: I 20 MET cc_start: 0.8238 (ppp) cc_final: 0.7970 (pmm) REVERT: I 21 ARG cc_start: 0.8415 (tpp-160) cc_final: 0.8174 (tpp-160) outliers start: 63 outliers final: 34 residues processed: 209 average time/residue: 0.4798 time to fit residues: 106.2849 Evaluate side-chains 197 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 159 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 90 CYS Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 254 TYR Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 267 GLN Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain E residue 43 ARG Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain H residue 52 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 51 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 61 optimal weight: 0.0980 chunk 65 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 47 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 ASN ** H 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.202251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.157731 restraints weight = 7717.423| |-----------------------------------------------------------------------------| r_work (start): 0.4252 rms_B_bonded: 2.62 r_work: 0.4106 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.4106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 7042 Z= 0.158 Angle : 0.816 13.810 9509 Z= 0.406 Chirality : 0.048 0.253 1062 Planarity : 0.005 0.053 1199 Dihedral : 7.771 58.571 991 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 5.98 % Allowed : 40.49 % Favored : 53.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.30), residues: 852 helix: 1.44 (0.32), residues: 263 sheet: -0.55 (0.26), residues: 392 loop : -0.55 (0.49), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 239 TYR 0.014 0.001 TYR H 33 PHE 0.031 0.001 PHE G 27 TRP 0.008 0.001 TRP A 259 HIS 0.003 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 7042) covalent geometry : angle 0.81577 ( 9509) hydrogen bonds : bond 0.03522 ( 452) hydrogen bonds : angle 5.58721 ( 1299) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 165 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.5555 (pp20) cc_final: 0.4912 (tm-30) REVERT: A 98 MET cc_start: 0.7701 (OUTLIER) cc_final: 0.7298 (ttm) REVERT: A 265 LEU cc_start: 0.8271 (mm) cc_final: 0.7920 (mm) REVERT: A 270 MET cc_start: 0.7092 (ttm) cc_final: 0.6888 (ttt) REVERT: B 96 ILE cc_start: 0.6686 (OUTLIER) cc_final: 0.6316 (pp) REVERT: B 154 MET cc_start: 0.7153 (ttp) cc_final: 0.6922 (ttp) REVERT: B 167 GLN cc_start: 0.6632 (OUTLIER) cc_final: 0.6416 (tp-100) REVERT: B 250 LEU cc_start: 0.6845 (mp) cc_final: 0.6304 (tp) REVERT: B 254 TYR cc_start: 0.7242 (OUTLIER) cc_final: 0.6132 (m-80) REVERT: C 72 PHE cc_start: 0.7191 (OUTLIER) cc_final: 0.6731 (t80) REVERT: C 76 LYS cc_start: 0.7554 (mmtm) cc_final: 0.7138 (mmpt) REVERT: D 77 MET cc_start: 0.5265 (tpt) cc_final: 0.4582 (mtm) REVERT: D 82 ARG cc_start: 0.4130 (tmt-80) cc_final: 0.1384 (mmt180) REVERT: E 43 ARG cc_start: 0.6928 (OUTLIER) cc_final: 0.5769 (ptt180) REVERT: E 57 TRP cc_start: 0.6742 (t60) cc_final: 0.6309 (t60) REVERT: E 60 ARG cc_start: 0.5936 (mtt90) cc_final: 0.5448 (mtt90) REVERT: G 44 MET cc_start: 0.3432 (pp-130) cc_final: 0.2440 (pmm) outliers start: 44 outliers final: 29 residues processed: 193 average time/residue: 0.4826 time to fit residues: 98.6901 Evaluate side-chains 198 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 163 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain B residue 90 CYS Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 254 TYR Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain E residue 43 ARG Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 52 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 34 optimal weight: 5.9990 chunk 46 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 HIS A 321 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.199037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.156057 restraints weight = 7707.486| |-----------------------------------------------------------------------------| r_work (start): 0.4238 rms_B_bonded: 2.92 r_work: 0.4064 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.4064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.4287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 7042 Z= 0.204 Angle : 0.879 16.709 9509 Z= 0.439 Chirality : 0.049 0.289 1062 Planarity : 0.005 0.052 1199 Dihedral : 7.982 59.407 991 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 5.71 % Allowed : 41.44 % Favored : 52.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.30), residues: 852 helix: 1.25 (0.33), residues: 264 sheet: -0.58 (0.26), residues: 394 loop : -0.53 (0.49), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 38 TYR 0.010 0.002 TYR B 221 PHE 0.035 0.002 PHE D 101 TRP 0.011 0.001 TRP A 259 HIS 0.008 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00486 ( 7042) covalent geometry : angle 0.87942 ( 9509) hydrogen bonds : bond 0.03814 ( 452) hydrogen bonds : angle 5.77623 ( 1299) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 163 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.7733 (OUTLIER) cc_final: 0.7321 (ttm) REVERT: A 265 LEU cc_start: 0.8409 (mm) cc_final: 0.8108 (mm) REVERT: A 270 MET cc_start: 0.7300 (ttm) cc_final: 0.7078 (ttt) REVERT: B 250 LEU cc_start: 0.7007 (mp) cc_final: 0.6497 (tp) REVERT: C 72 PHE cc_start: 0.7178 (OUTLIER) cc_final: 0.6753 (t80) REVERT: C 76 LYS cc_start: 0.7607 (mmtm) cc_final: 0.7190 (mmpt) REVERT: D 77 MET cc_start: 0.5410 (tpt) cc_final: 0.4762 (mtm) REVERT: D 82 ARG cc_start: 0.4426 (tmt-80) cc_final: 0.3654 (mmm160) REVERT: E 43 ARG cc_start: 0.7030 (OUTLIER) cc_final: 0.5712 (ptt180) REVERT: E 57 TRP cc_start: 0.6786 (t60) cc_final: 0.6572 (t60) REVERT: F 49 LEU cc_start: 0.7101 (mt) cc_final: 0.6847 (tt) REVERT: G 44 MET cc_start: 0.3484 (pp-130) cc_final: 0.2596 (pmm) REVERT: I 20 MET cc_start: 0.8304 (ppp) cc_final: 0.7945 (pmm) REVERT: J 28 ILE cc_start: 0.9017 (tp) cc_final: 0.8737 (tp) outliers start: 42 outliers final: 31 residues processed: 189 average time/residue: 0.5006 time to fit residues: 100.2589 Evaluate side-chains 197 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 163 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 90 CYS Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 254 TYR Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 267 GLN Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain E residue 43 ARG Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain H residue 12 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 chunk 3 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 HIS A 321 ASN ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4683 r_free = 0.4683 target = 0.199249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.155724 restraints weight = 7751.534| |-----------------------------------------------------------------------------| r_work (start): 0.4232 rms_B_bonded: 2.81 r_work: 0.4058 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.4058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.4392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 7042 Z= 0.199 Angle : 0.892 16.371 9509 Z= 0.448 Chirality : 0.050 0.284 1062 Planarity : 0.005 0.053 1199 Dihedral : 8.068 58.693 991 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 5.57 % Allowed : 41.58 % Favored : 52.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.30), residues: 852 helix: 1.13 (0.33), residues: 264 sheet: -0.61 (0.27), residues: 396 loop : -0.48 (0.49), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 239 TYR 0.016 0.002 TYR B 237 PHE 0.051 0.002 PHE D 101 TRP 0.010 0.001 TRP A 259 HIS 0.007 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00475 ( 7042) covalent geometry : angle 0.89198 ( 9509) hydrogen bonds : bond 0.03833 ( 452) hydrogen bonds : angle 5.81822 ( 1299) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3048.75 seconds wall clock time: 52 minutes 39.98 seconds (3159.98 seconds total)